Herzog's other work has very similar themes, he hasn't matched the heights of Aguirre, but he's always interesting and mostly spot on. Also possesses a very confronting sense of humour which can have you in stitches at times.

Lessons of Darkness, The Enigma of Kasper Hauser and the downright hilarious Even Dwarfs Started of Small are the closest to Aguirre in quality in my eyes.

Haven't seen Aguirre, but I've watched some early shorts by Herzog recently. Here in germany his films are relatively easy to come by - but mabe that's a reason why I have seen so little, yet.
My favorite so far is Woyzeck (197 . Kinski is great as usual, but the really outstanding event is the best closing shot I've ever seen. Simply eye-popping.

I was rather disappointed with Woyczek. Fitzcarraldo is a perfect companion piece for Aguirre, the two films are inextricably linked imo. As far as Herzog's next best film, I would vote for Cobra Verde, but I'm yet to find anyone who agrees with me.

I've just ordered a few more films from him, including two documentaries, so hopefully I can shed a little more light on his lesser seen films. I found Stroszek difficult at parts, which might be why you enjoyed it. Hard to say what faults I had with it, but it just left me cold.

I tend to have a preference for those films ("Kaspar Hauser", "Stroszek", "Heart of Glass" and "Even Dwarfs Started Small") that do not have Kinski (though he was a hell of an actor, and, perhaps, because of it one's attention is centred on the manic protaonists he essays!) because they allow the viewer's attention to wander to other things that are as important to Herzog as his protagonist. "Stroszek" is a difficult film, but the manner in which it slowly builds up to that climactic sequence of the dancing chicken in an otherwise desolate landscape, is phenomenal. That last image, at once a shocking finale to an otherwise understated film, and a befitting culmination of everything that preceded it, makes "Stroszek" stand out.

Stroszek is strong, but not as inconclusive or as abstract as some of his other films. I get a bit tired of his recurring motifs sometimes and i preferred the way the chicken was used in Dwarfs. Also, third time in 7 years he used the spinning car motif, gets a little repetitive after a while.